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Gentica277282
02-02-2022, 10:05 PM
I thought it would be interesting to see the differences between qpadm and g25, thanks to mnemonics for running me on qpadm


left pops:
Dante
Iberomaurusian
Anatolia_N
Germany_CordedWare
Congo_Kindoki_Protohistoric

right pops:
Cameroon_SMA.SG
DevilsGate_N
South_Africa_HG
Yana_UP
Boncuklu_N.SG
Bahamas_SouthAndros_Ceramic.SG
CHG
Iran_Wezmeh_N.SG
Ekven_IA.SG
Mota
Swiss_HG

0 Dante 1
1 Iberomaurusian 6
2 Anatolia_N 25
3 Germany_CordedWare 9
4 Congo_Kindoki_Protohistoric 2
5 Cameroon_SMA.SG 2
6 DevilsGate_N 4
7 South_Africa_HG 4
8 Yana_UP 2
9 Boncuklu_N.SG 6
10 Bahamas_SouthAndros_Ceramic.SG 4
11 CHG 2
12 Iran_Wezmeh_N.SG 1
13 Ekven_IA.SG 10
14 Mota 1
15 Swiss_HG 1
jackknife block size: 0.050
snps: 1150527 indivs: 80
number of blocks for block jackknife: 714
## ncols: 1150527
coverage: Dante 1149230
coverage: Iberomaurusian 1088044
coverage: Anatolia_N 1121996
coverage: Germany_CordedWare 885285
coverage: Congo_Kindoki_Protohistoric 700438
coverage: Cameroon_SMA.SG 1148760
coverage: DevilsGate_N 1134715
coverage: South_Africa_HG 1135129
coverage: Yana_UP 1135189
coverage: Boncuklu_N.SG 1138952
coverage: Bahamas_SouthAndros_Ceramic.SG 1150077
coverage: CHG 1134595
coverage: Iran_Wezmeh_N.SG 1148603
coverage: Ekven_IA.SG 1144810
coverage: Mota 1134612
coverage: Swiss_HG 1130733
Effective number of blocks: 618.649
numsnps used: 669425
codimension 1
f4info:
f4rank: 3 dof: 7 chisq: 39.775 tail: 1.39016878e-06 dofdiff: 9 chisqdiff: -39.775 taildiff: 1
B:
scale 1.000 1.000 1.000
DevilsGate_N 0.972 -0.375 1.032
South_Africa_HG -0.049 0.077 -1.270
Yana_UP 1.056 -0.101 1.160
Boncuklu_N.SG 1.293 2.807 1.111
Bahamas_SouthAndros_Ceramic.SG 1.053 -1.016 -0.586
CHG 1.175 0.180 -1.054
Iran_Wezmeh_N.SG 1.064 0.442 -0.191
Ekven_IA.SG 1.028 -0.786 -0.121
Mota 0.166 -0.174 1.620
Swiss_HG 1.250 -0.232 -0.781
A:
scale 80.647 1170.238 2308.660
Iberomaurusian -0.127 -0.737 1.280
Anatolia_N 0.772 1.603 -0.376
Germany_CordedWare 0.909 -0.936 -1.116
Congo_Kindoki_Protohistoric -1.600 0.105 -0.987


full rank
f4info:
f4rank: 4 dof: 0 chisq: 0.000 tail: 1 dofdiff: 7 chisqdiff: 39.775 taildiff: 1.39016878e-06
B:
scale 583.602 98.969 88.579 49.022
DevilsGate_N -0.227 0.878 0.962 -0.994
South_Africa_HG -0.026 0.014 0.009 0.071
Yana_UP -0.093 1.035 1.050 -1.056
Boncuklu_N.SG -1.582 1.630 1.070 -1.292
Bahamas_SouthAndros_Ceramic.SG -0.548 0.908 1.177 -1.041
CHG -1.542 1.152 1.194 -1.164
Iran_Wezmeh_N.SG -1.702 1.037 0.986 -1.086
Ekven_IA.SG -0.443 0.909 1.115 -1.021
Mota 0.472 0.093 0.085 -0.232
Swiss_HG -1.200 1.199 1.338 -1.228
A:
scale 2.000 2.000 2.000 2.000
Iberomaurusian 2.000 0.000 0.000 0.000
Anatolia_N 0.000 2.000 0.000 0.000
Germany_CordedWare 0.000 0.000 2.000 0.000
Congo_Kindoki_Protohistoric 0.000 0.000 0.000 2.000


best coefficients: 0.375 0.260 0.172 0.193
Jackknife mean: 0.373331574 0.260499286 0.172157340 0.194011800
std. errors: 0.070 0.026 0.042 0.029

error covariance (* 1,000,000)
4924 -588 -2359 -1977
-588 700 -334 222
-2359 -334 1780 914
-1977 222 914 841


summ: Dante 4 0.000001 0.373 0.260 0.172 0.194 4924 -588 -2359 -1977 700 ...
-334 222 1780 914 841

fixed pat wt dof chisq tail prob
0000 0 7 39.775 1.39017e-06 0.375 0.260 0.172 0.193
0001 1 8 71.543 2.42102e-12 0.829 0.205 -0.033 0.000 infeasible
0010 1 8 55.521 3.4956e-09 0.594 0.296 0.000 0.110
0100 1 8 116.871 1.46578e-21 0.723 0.000 0.219 0.057
1000 1 8 68.038 1.20682e-11 0.000 0.310 0.346 0.344
0011 2 9 168.322 0 0.848 0.152 0.000 0.000
0101 2 9 300.763 0 0.876 0.000 0.124 0.000
0110 2 9 191.637 0 1.079 0.000 0.000 -0.079 infeasible
1001 2 9 1462.326 0 0.000 -81.687 82.687 0.000 infeasible
1010 2 9 260.957 0 0.000 0.637 0.000 0.363
1100 2 9 184.735 0 0.000 0.000 0.653 0.347
0111 3 10 168.416 0 1.000 0.000 0.000 0.000
1011 3 10 2613.022 0 0.000 1.000 0.000 0.000
1101 3 10 1855.322 0 0.000 0.000 1.000 0.000
1110 3 10 4446.912 0 0.000 0.000 0.000 1.000
best pat: 0000 1.39017e-06 - -
best pat: 0010 3.4956e-09 chi(nested): 15.747 p-value for nested model: 7.2409e-05
best pat: 0011 1.3799e-31 chi(nested): 112.800 p-value for nested model: 2.38638e-26
best pat: 0111 5.90235e-31 chi(nested): 0.094 p-value for nested model: 0.759015

coeffs: 0.375 0.260 0.172 0.193

## dscore:: f_4(Base, Fit, Rbase, right2)
## genstat:: f_4(Base, Fit, right1, right2)

details: Iberomaurusian DevilsGate_N -0.000390 -0.985557
details: Anatolia_N DevilsGate_N 0.008874 26.016889
details: Germany_CordedWare DevilsGate_N 0.010864 28.128407
details: Congo_Kindoki_Protohistoric DevilsGate_N -0.020274 -45.844157
dscore: DevilsGate_N f4: 0.000107 Z: 0.341866

details: Iberomaurusian South_Africa_HG -0.000044 -0.182045
details: Anatolia_N South_Africa_HG 0.000139 0.762589
details: Germany_CordedWare South_Africa_HG 0.000100 0.454818
details: Congo_Kindoki_Protohistoric South_Africa_HG 0.001452 5.459197
dscore: South_Africa_HG f4: 0.000317 Z: 1.776773

details: Iberomaurusian Yana_UP -0.000159 -0.386863
details: Anatolia_N Yana_UP 0.010462 31.196911
details: Germany_CordedWare Yana_UP 0.011858 31.349107
details: Congo_Kindoki_Protohistoric Yana_UP -0.021546 -49.460616
dscore: Yana_UP f4: 0.000531 Z: 1.697208

details: Iberomaurusian Boncuklu_N.SG -0.002711 -6.619793
details: Anatolia_N Boncuklu_N.SG 0.016470 47.494314
details: Germany_CordedWare Boncuklu_N.SG 0.012083 31.284116
details: Congo_Kindoki_Protohistoric Boncuklu_N.SG -0.026355 -59.914940
dscore: Boncuklu_N.SG f4: 0.000245 Z: 0.757945

details: Iberomaurusian Bahamas_SouthAndros_Ceramic.SG -0.000939 -2.305969
details: Anatolia_N Bahamas_SouthAndros_Ceramic.SG 0.009172 26.779290
details: Germany_CordedWare Bahamas_SouthAndros_Ceramic.SG 0.013290 34.517876
details: Congo_Kindoki_Protohistoric Bahamas_SouthAndros_Ceramic.SG -0.021245 -48.720518
dscore: Bahamas_SouthAndros_Ceramic.SG f4: 0.000207 Z: 0.656384

details: Iberomaurusian CHG -0.002642 -6.239881
details: Anatolia_N CHG 0.011637 32.538898
details: Germany_CordedWare CHG 0.013478 32.899610
details: Congo_Kindoki_Protohistoric CHG -0.023741 -52.140996
dscore: CHG f4: -0.000240 Z: -0.716464

details: Iberomaurusian Iran_Wezmeh_N.SG -0.002917 -6.343347
details: Anatolia_N Iran_Wezmeh_N.SG 0.010478 26.924598
details: Germany_CordedWare Iran_Wezmeh_N.SG 0.011131 25.477544
details: Congo_Kindoki_Protohistoric Iran_Wezmeh_N.SG -0.022147 -45.784191
dscore: Iran_Wezmeh_N.SG f4: -0.000740 Z: -2.032744

details: Iberomaurusian Ekven_IA.SG -0.000759 -1.973688
details: Anatolia_N Ekven_IA.SG 0.009186 27.973097
details: Germany_CordedWare Ekven_IA.SG 0.012591 34.282226
details: Congo_Kindoki_Protohistoric Ekven_IA.SG -0.020837 -49.534443
dscore: Ekven_IA.SG f4: 0.000238 Z: 0.787416

details: Iberomaurusian Mota 0.000808 2.588997
details: Anatolia_N Mota 0.000943 3.790377
details: Germany_CordedWare Mota 0.000955 3.304021
details: Congo_Kindoki_Protohistoric Mota -0.004727 -13.768263
dscore: Mota f4: -0.000201 Z: -0.864633

details: Iberomaurusian Swiss_HG -0.002057 -4.226702
details: Anatolia_N Swiss_HG 0.012119 30.641132
details: Germany_CordedWare Swiss_HG 0.015106 32.520967
details: Congo_Kindoki_Protohistoric Swiss_HG -0.025045 -48.775783
dscore: Swiss_HG f4: 0.000132 Z: 0.350053

gendstat: Cameroon_SMA.SG DevilsGate_N 0.342
gendstat: Cameroon_SMA.SG South_Africa_HG 1.777
gendstat: Cameroon_SMA.SG Yana_UP 1.697
gendstat: Cameroon_SMA.SG Boncuklu_N.SG 0.758
gendstat: Cameroon_SMA.SG Bahamas_SouthAndros_Ceramic.SG 0.656
gendstat: Cameroon_SMA.SG CHG -0.716
gendstat: Cameroon_SMA.SG Iran_Wezmeh_N.SG -2.033
gendstat: Cameroon_SMA.SG Ekven_IA.SG 0.787
gendstat: Cameroon_SMA.SG Mota -0.865
gendstat: Cameroon_SMA.SG Swiss_HG 0.350
gendstat: DevilsGate_N South_Africa_HG 0.670
gendstat: DevilsGate_N Yana_UP 1.672
gendstat: DevilsGate_N Boncuklu_N.SG 0.549
gendstat: DevilsGate_N Bahamas_SouthAndros_Ceramic.SG 0.439
gendstat: DevilsGate_N CHG -1.303
gendstat: DevilsGate_N Iran_Wezmeh_N.SG -2.681
gendstat: DevilsGate_N Ekven_IA.SG 0.635
gendstat: DevilsGate_N Mota -0.952
gendstat: DevilsGate_N Swiss_HG 0.077
gendstat: South_Africa_HG Yana_UP 0.675
gendstat: South_Africa_HG Boncuklu_N.SG -0.224
gendstat: South_Africa_HG Bahamas_SouthAndros_Ceramic.SG -0.350
gendstat: South_Africa_HG CHG -1.671
gendstat: South_Africa_HG Iran_Wezmeh_N.SG -2.856
gendstat: South_Africa_HG Ekven_IA.SG -0.261
gendstat: South_Africa_HG Mota -2.082
gendstat: South_Africa_HG Swiss_HG -0.488
gendstat: Yana_UP Boncuklu_N.SG -1.194
gendstat: Yana_UP Bahamas_SouthAndros_Ceramic.SG -1.263
gendstat: Yana_UP CHG -2.825
gendstat: Yana_UP Iran_Wezmeh_N.SG -4.178
gendstat: Yana_UP Ekven_IA.SG -1.252
gendstat: Yana_UP Mota -2.220
gendstat: Yana_UP Swiss_HG -1.291
gendstat: Boncuklu_N.SG Bahamas_SouthAndros_Ceramic.SG -0.151
gendstat: Boncuklu_N.SG CHG -1.945
gendstat: Boncuklu_N.SG Iran_Wezmeh_N.SG -3.443
gendstat: Boncuklu_N.SG Ekven_IA.SG -0.033
gendstat: Boncuklu_N.SG Mota -1.328
gendstat: Boncuklu_N.SG Swiss_HG -0.392
gendstat: Bahamas_SouthAndros_Ceramic.SG CHG -1.653
gendstat: Bahamas_SouthAndros_Ceramic.SG Iran_Wezmeh_N.SG -3.084
gendstat: Bahamas_SouthAndros_Ceramic.SG Ekven_IA.SG 0.169
gendstat: Bahamas_SouthAndros_Ceramic.SG Mota -1.263
gendstat: Bahamas_SouthAndros_Ceramic.SG Swiss_HG -0.238
gendstat: CHG Iran_Wezmeh_N.SG -1.667
gendstat: CHG Ekven_IA.SG 1.906
gendstat: CHG Mota 0.115
gendstat: CHG Swiss_HG 1.193
gendstat: Iran_Wezmeh_N.SG Ekven_IA.SG 3.345
gendstat: Iran_Wezmeh_N.SG Mota 1.457
gendstat: Iran_Wezmeh_N.SG Swiss_HG 2.472
gendstat: Ekven_IA.SG Mota -1.408
gendstat: Ekven_IA.SG Swiss_HG -0.351
gendstat: Mota Swiss_HG 0.872

Aben Aboo
02-02-2022, 11:01 PM
Interesting, but personally i don't understand very well the results, lol